Singapore said Tuesday it will ban from its ports and naval bases an Indonesian navy ship named after two marines who bombed an office complex in the city-state in the 1960s.

Defence Minister Ng Eng Hen said the ship will be barred as part of a dispute over the Indonesian navy's decision to name the refurbished frigate after the two marines, Usman Haji Mohamed Ali and Harun Said.

They were convicted and executed in Singapore for the bombing in March 1965 which killed three people and injured 33 others.

But the marines, who had entered Singapore in civilian disguise, have been hailed as heroes in Indonesia.

Their undercover infiltration was part of an attempt by then-Indonesian president Sukarno to stage an armed confrontation against the newly formed federation of Malaysia, which at the time included Singapore.

"Singapore will not allow this military ship named Usman Harun to call at our ports and naval bases," Ng told parliament Tuesday.

"It will not be possible for the SAF (Singapore Armed Forces) as protectors of this nation to sail alongside or exercise with this ship."

In an emotionally charged speech, Ng said the defence ministry and the SAF were "disappointed and dismayed at this inexplicable move".

"Even without ill intent, how can the naming of the ship after two bombers build good ties or enhance mutual respect and regard with both our countries?" he said.

Responding to the ban, Indonesian security minister Djoko Suyanto said: "The ship has not even arrived yet, so what's the fuss?"

"Anyway, who says the ship will be taken to Singapore?" he told AFP by text message in Jakarta.

Indonesia Foreign Minister Marty Natalegawa reiterated earlier comments that his country had no "bad intention" in naming the ship after the two marines.

"The problem comes from a different understanding and different perception," he told reporters in Jakarta.

"Why don't we just accept these different opinions? We should not continue with this process, or the dispute will intensify. It is not necessary."

Singapore's Ng said the Indonesian vessel's presence on the high seas would be a "constant reminder of the military aggression and atrocious crimes committed by the Indonesian marines who killed or irreparably damaged the lives of innocent civilians and their families in Singapore".

He added however that Singapore would not "overread and jump at shadows" over Indonesia's move, and would look to rebuild good military ties with its larger neighbour.

In a separate statement also in parliament, Singaporean Foreign Minister K. Shanmugam said the city-state had sent Jakarta a formal protest note over the issue.

He said Singapore would take Natalegawa at his word "that there was no ill-will and there was no malice and that it (the naming of the ship) was a decision taken at a professional level".

"The Indonesians consider Usman and Harun heroes. But for Singaporeans, in particular the victims and their families, their action was criminal, not heroic," Shanmugam said.

"The warship will travel to different places, bringing painful memories wherever it goes."

Singapore, which acrimoniously split from Malaysia to become an independent state in 1965, and Indonesia are members of the Association of Southeast Asian Nations.

Indonesia is Singapore's third largest trading partner, with total bilateral trade reaching Sg$79.4 billion ($62.6 billion) in 2012.

Relations hit a low point in the late 1990s after the fall of former dictator Suharto, and his successor B.J. Habibie famously referred to the tiny city-state as a "little red dot" on the map.

Ties have improved considerably in recent years.

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